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Number of items: 77. 2019Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul . (Submitted) Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848 2018Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogen-bond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). -244504. ISSN 0021-9606, ESSN: 1089-7690 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690 Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524 (Unpublished) Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 1-22. ISSN 2353-6438 (online) Heida, M. and Patterson, R. I. A and Renger, M. (2018) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. J. Evol. Equ. . pp. 1-42. ISSN Online: 1424-3202 Print: 1424-3199 Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 1261-1326. ISSN 0022-4715 Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690 del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). ISSN 0021-9606, ESSN: 1089-7690 Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 1915-1957. ISSN 1432-1467 (online) Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 1-29. (Unpublished) Patterson, R. I. A and Renger, M. (2018) Large deviations of reaction fluxes. SFB 1114 Preprint in arXiv:1802.02512 . pp. 1-21. (Unpublished) Schulz, R. and Hansen, Y. von and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water. SFB 1114 Preprint 02/2018 . (Unpublished) Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690 Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137-164. ISSN 0935-4964 (Print) 1432-2250 (Online) 2017Heida, M. and Kornhuber, R. and Podlesny, J. (2017) Fractal homogenization of multiscale interface problems. SFB 1114 Preprint in arXiv . pp. 1-17. (Submitted) Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) Liero, M. and Mielke, A. and Savaré, G. (2017) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Invent. math. . pp. 1-149. ISSN 1432-1297 (online) Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) Kappler, J. and Shrivastava, S. and Schneider, M.F. and Netz, R.R. (2017) Nonlinear fractional waves at elastic interfaces. Phys. Rev. Fluids, 2 (11). p. 114804. Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095). Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global well-posedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715 Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2017) The Dynamic State Index with Moisture and Phase Changes. SFB 1114 Preprint . pp. 1-12. (Unpublished) Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Heida, M. (2017) On Convergences of square-root approximation scheme to Fokker--Planck operator. SFB 1114 Preprint at WIAS 05/2017 . pp. 1-30. (Unpublished) Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084 Heida, M. (2017) Stochastic homogenization of rate-independent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853-894. ISSN 1432-0959 (online) 0935-1175 (print) Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and Blume-Peytavi, U. and Hedtrich, S. and Schäfer-Korting, M. and Rühl, E. and Netz, R.R. (2017) Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles. PNAS, 114 (14). pp. 3631-3636. ISSN 1091-6490 (online) Gussmann, P. and Mielke, A. (2017) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Adv. Calc. Var. . (Submitted) Flegel, F. and Heida, M. and Slowik, M. (2017) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. SFB 1114 Preprint in arXiv:1702.02860 . (Unpublished) Heida, M. and Schweizer, B. (2017) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations . pp. 1-30. (Submitted) Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2017) On microscopic origins of generalized gradient structures. Discrete and Continuous Dynamical Systems - Series S, 10 (1). Heida, M. and Nesenenko, S. (2017) Stochastic homogenization of rate-dependent models of monotone type in plasticity. SFB 1114 Preprint in arXiv:1701.03505 . pp. 1-26. (Unpublished) Heida, M. and Mielke, A. (2017) Averaging of time-periodic dissipation potentials in rate-independent processes. Discrete and Continuous Dynamical Systems - Series S, 10 (6). pp. 1303-1327. Mielke, A. (2017) Three examples concerning the interaction of dry friction and oscillations. In: Trends on Application of Mathematics to Mechanics. Springer INdAM series. (In Press) Mielke, A. and Mittnenzweig, M. (2017) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270. Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934. Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873. Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953 2016Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46. Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321). Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rate-independent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 54-69. Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The Hellinger--Kantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 2869-2911. ISSN 1095-7154 (online) Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424 Mielke, A. and Peletier, M. A. and Renger, M. (2016) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics, 41 (2). Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130). Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34. Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27. Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309. 2015Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101. Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002. Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606 Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355 Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355 Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630 Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89). Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499. Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542. |